Abstract. We present a global distribution of surface methane (CH₄) emission estimates for 2000–2012 derived using the CarbonTracker Europe-CH₄ (CTE-CH₄) data assimilation system. In CTE-CH₄, anthropogenic and biospheric CH₄ emissions are simultaneously estimated based on constraints of global atmospheric in situ CH₄ observations. The system was configured to either estimate only anthropogenic or biospheric sources per region, or to estimate both categories simultaneously. The latter increased the number of optimizable parameters from 62 to 78. In addition, the differences between two numerical schemes available to perform turbulent vertical mixing in the atmospheric transport model TM5 were examined. Together, the system configurations encompass important axes of uncertainty in inversions and allow us to examine the robustness of the flux estimates. The posterior emission estimates are further evaluated by comparing simulated atmospheric CH₄ to surface in situ observations, vertical profiles of CH₄ made by aircraft, remotely sensed dry-air total column-averaged mole fraction (XCH₄) from the Total Carbon Column Observing Network (TCCON), and XCH₄ from the Greenhouse gases Observing Satellite (GOSAT). The evaluation with non-assimilated observations shows that posterior XCH₄ is better matched with the retrievals when the vertical mixing scheme with faster interhemispheric exchange is used. Estimated posterior mean total global emissions during 2000–2012 are 516 ± 51 Tg CH₄ yr⁻¹, with an increase of 18 Tg CH₄ yr⁻¹ from 2000–2006 to 2007–2012. The increase is mainly driven by an increase in emissions from South American temperate, Asian temperate and Asian tropical TransCom regions. In addition, the increase is hardly sensitive to different model configurations ( <  2 Tg CH₄ yr⁻¹ difference), and much smaller than suggested by EDGAR v4.2 FT2010 inventory (33 Tg CH₄ yr⁻¹), which was used for prior anthropogenic emission estimates. The result is in good agreement with other published estimates from inverse modelling studies (16–20 Tg CH₄ yr⁻¹). However, this study could not conclusively separate a small trend in biospheric emissions (−5 to +6.9 Tg CH₄ yr⁻¹) from the much larger trend in anthropogenic emissions (15–27 Tg CH₄ yr⁻¹). Finally, we find that the global and North American CH₄ balance could be closed over this time period without the previously suggested need to strongly increase anthropogenic CH₄ emissions in the United States. With further developments, especially on the treatment of the atmospheric CH₄ sink, we expect the data assimilation system presented here will be able to contribute to the ongoing interpretation of changes in this important greenhouse gas budget.